Honest question: What choices can you make that affect the world in base Fallout 4? There's the faction you choose which affects the ending, there's base building that causes NPCs to show up and provide you resources (but don't otherwise affect the narrative), and...?

Aside from the somewhat cosmetic things like, the arrival of the Pryddwen and the way the Cambridge Police Station changes as you progress in the Brotherhood quests, stuff like that, you can also kill named NPCs and they are just gone and don't come back, and their quests are gone etc.